Can my employees see the special airline and hotel rates my company has negotiated instead of the normal public prices?

Yes, in most cases they can, but it depends on where that deal actually sits. When a company agrees special rates with an airline or a hotel chain, those rates are usually tied to an account code or a contract reference. The booking system can carry that code with every search your staff run, so the agreed price comes back to them instead of, or alongside, the fare any member of the public would see.

How cleanly this works comes down to the supplier and the connection you are using. Some airline and hotel connections accept a negotiated rate code and return your prices without any fuss. Others only release the agreed rate on a separate feed, or only to the party that signed the contract, and in that case your staff will see the public price and nothing more. So before you tell everyone their corporate rate will appear, it is worth asking each supplier what they actually support on the connection you have.

You can normally control who sees which deal as well. If different departments, or different companies within the same group, hold different agreements, the rates can be attached to the traveller's company or profile, so people only ever see what their own employer negotiated and the rest stays hidden from them.

The part people forget is the paperwork. These contracts get reviewed, and a code that has quietly expired will drop your staff straight back to public prices without anyone noticing. Ask your supplier contact to confirm the code and the dates it is valid for, then have it loaded and tested with a real search before you announce it to your travellers.